stc1 (SPBP8B7.28c)


Gene Standard Namestc1 Characterisation Statuspublished
Systematic IDSPBP8B7.28c Feature Typeprotein coding
Synonyms Name DescriptionSiRNA To Chromatin
ProductLIM-like protein linking chromatin modification to RNAi, Stc1 Product Size215aa, 25.07 kDa
Genomic Location Chromosome II, 3691942-3691008 (935nt); CDS:3691848-3691201 (648nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
protein binding872
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
GO Cellular Component
Term NameCount
CLRC ubiquitin ligase complex6
Annotation ExtensionEvidenceWith/FromReference
nuclear pericentric heterochromatin42
Annotation ExtensionEvidenceWith/FromReference
nucleolus365
Annotation ExtensionEvidenceWith/FromReference
nucleus2691
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Viable

Population Phenotype

Term NameGenotypesCount
sensitive to bortezomibstc1Δ255
sensitive to camptothecinstc1Δ248
sensitive to thiabendazolestc1Δ327
slow vegetative cell population growthstc1Δ361
viable vegetative cell populationstc1Δ3844

Cell Phenotype

Term NameGenotypesCount
abnormal actin cortical patch localizationstc1Δ62
abnormal actin cytoskeleton during vegetative growthstc1Δ53
abnormal meiosisstc1Δ121
abolished histone H3-K9 dimethylation at centromerestc1Δ2
centromeric outer repeat transcript-derived siRNA absentstc1Δ8
decreased chromatin silencing at centromere outer repeatstc1Δ48
decreased histone H3-K9 dimethylation at centromere outer repeatstc1Δ11
decreased protein localization to heterochromatin at centromere outer repeat11
affects localization of swi6stc1Δ
increased minichromosome loss upon segregation during vegetative growthstc1Δ19
lagging mitotic chromosomesstc1Δ40
normal centromeric outer repeat transcript-derived siRNA levelstc1Δ8
normal chromatin silencing at silent mating-type cassettestc1Δ22
normal chromatin silencing at telomerestc1Δ16
viable curved vegetative cellstc1Δ70
Target Of
OntologyRelationshipGeneProduct
FYPO localization affected by mutation in chp1 chromodomain protein Chp1
FYPO localization affected by mutation in clr3 histone deacetylase (class II) Clr3
FYPO localization affected by mutation in dcr1 dicer
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons3691942..3691008
mRNA3691942..3691008
5' UTR3691942..3691849PMID:21511999
CDS3691848..3691201
3' UTR3691200..3691008PMID:21511999
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF12898 Pfam IPR024630 Stc1 domain 42 122 1

View domain organization at Pfam

Protein Properties

Ave. residue weight 116.63 Da
Charge -3.00
Codon Adaptation Index 0.40
Isoelectric point 5.69
Molecular weight 25.07 kDa
Number of residues 215
Modifications

Protein Modifications

Term NameResidueCount
O-phospho-L-serine 1677
present during mitotic M phaseS169
present during mitotic M phaseS146
S146
Annotation ExtensionEvidenceResidueReference
present during mitotic M phase experimental evidence S169 PMID:21712547
present during mitotic M phase experimental evidence S146 PMID:21712547
experimental evidence S146 PMID:24763107
O-phospho-L-threonine 701
present during mitotic M phaseT172
Annotation ExtensionEvidenceResidueReference
present during mitotic M phase experimental evidence T172 PMID:21712547
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for stc1 (SPBP8B7.28c)

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
0.67during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
0.2during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
no apparent S. cerevisiae ortholog601
conserved in fungi only618
conserved in fungi4606
Orthologs

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBP8B7.28c into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
forms complex withrik1silencing protein Rik1 Reconstituted ComplexPMID:24449894
forms complex withago1argonaute Reconstituted ComplexPMID:20211136
forms complex withraf2Rik1-associated factor Raf2 Reconstituted ComplexPMID:24449894
affinity capturesraf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Affinity Capture-MSPMID:20211136
affinity capturespcu4cullin 4 Affinity Capture-MSPMID:20211136
affinity capturesrik1silencing protein Rik1 Affinity Capture-WesternPMID:20211136
affinity capturesraf2Rik1-associated factor Raf2 Affinity Capture-WesternPMID:23613586
affinity capturesstc1LIM-like protein linking chromatin modification to RNAi, Stc1 Affinity Capture-MSPMID:20211136
affinity capturesser1phosphoserine aminotransferase (predicted) Affinity Capture-MSPMID:20211136
affinity capturesnop58U3 snoRNP protein Nop58 (predicted) Affinity Capture-MSPMID:20211136
affinity capturesebp2rRNA processing protein Ebp2 (predicted) Affinity Capture-MSPMID:20211136
affinity capturesnop56U3 snoRNP protein Nop56 (predicted) Affinity Capture-MSPMID:20211136
affinity capturesago1argonaute Affinity Capture-WesternPMID:20211136
affinity capturesclr4histone H3 lysine methyltransferase Clr4 Affinity Capture-WesternPMID:20211136
affinity capturesmas5DNAJ domain protein Mas5 (predicted) Affinity Capture-MSPMID:20211136
affinity capturesned8ubiquitin-like protein modifier Ned8 Affinity Capture-MSPMID:20211136
affinity captured byers1RNA-silencing factor Ers1 Affinity Capture-WesternPMID:22733737
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPBP8B7.28c into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
positive genetic interaction withpar2protein phosphatase PP2A regulatory subunit B-56 Par2 Positive GeneticPMID:22681890
positive genetic interaction withhhp2serine/threonine protein kinase Hhp2 Positive GeneticPMID:22681890
positive genetic interaction withclr4histone H3 lysine methyltransferase Clr4 Positive GeneticPMID:22681890
positive genetic interaction withrad57RecA family ATPase Rad57/Rhp57 Positive GeneticPMID:22681890
positive genetic interaction withurk1uridine kinase/uracil phosphoribosyltransferase (predicted) Positive GeneticPMID:22681890
positive genetic interaction withvrp1verprolin Positive GeneticPMID:22681890
positive genetic interaction withfft3SMARCAD1 family ATP-dependent DNA helicase Fft3 Positive GeneticPMID:22681890
positive genetic interaction withtop1DNA topoisomerase I Positive GeneticPMID:22681890
positive genetic interaction withswd1Set1C complex subunit Swd1 Positive GeneticPMID:22681890
positive genetic interaction withrik1silencing protein Rik1 Positive GeneticPMID:22681890
positive genetic interaction withdsk1SR protein-specific kinase Dsk1 Positive GeneticPMID:22681890
positive genetic interaction withers1RNA-silencing factor Ers1 Positive GeneticPMID:22681890
positive genetic interaction withtrm10tRNA m(1)G methyltransferase Trm10 Positive GeneticPMID:22681890
positive genetic interaction withraf2Rik1-associated factor Raf2 Positive GeneticPMID:22681890
rescued byraf2Rik1-associated factor Raf2 Phenotypic SuppressionPMID:20211136
rescued byraf1CLRC ubiquitin E3 ligase complex specificiy factor Raf1/Dos1 Phenotypic SuppressionPMID:20211136
rescued byclr4histone H3 lysine methyltransferase Clr4 Phenotypic SuppressionPMID:20211136
rescued byrik1silencing protein Rik1 Phenotypic SuppressionPMID:20211136
rescued bysir2Sirtuin family histone deacetylase Sir2 Phenotypic SuppressionPMID:20211136
negative genetic interaction withsfp1transcription factor Sfp1 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withcyp7cyclophilin family peptidyl-prolyl cis-trans isomerase Cyp7 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withcdt2WD repeat protein Cdt2 Negative GeneticPMID:22681890
negative genetic interaction withsap14U2 snRNP-associated protein SF3B14 Sap14 Negative GeneticPMID:22681890
negative genetic interaction withgid7GID complex subunit Gid7 (predicted) Negative GeneticPMID:22681890
negative genetic interaction withlaf1Clr6 L associated factor 1 Laf1 Negative GeneticPMID:22681890
negative genetic interaction withtoe2transcription factor, zf-fungal binuclear cluster type (predicted) Negative GeneticPMID:22681890
negative genetic interaction witheso1sister chromatid cohesion protein/DNA polymerase eta Eso1 fusion protein Negative GeneticPMID:23050226
negative genetic interaction withnsk1Clp1-interacting, microtubule plus-end binding Nsk1 Negative GeneticPMID:22681890
synthetically rescued bymst2histone acetyltransferase Mst2 Synthetic RescuePMID:21289066
rescuesclr4histone H3 lysine methyltransferase Clr4 Phenotypic SuppressionPMID:20211136
External References
Database Identifier Description
NBRP SPBP8B7.28c Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBP8B7.28c Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBP8B7.28c BioGRID Interaction Datasets
Expression Viewer SPBP8B7.28c Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBP8B7.28c Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBP8B7.28c Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBP8B7.28c Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBP8B7.28c Polyadenylation Viewer (Gullerova lab)
pombeTV SPBP8B7.28c Transcriptome Viewer (Bähler Lab)
GEO SPBP8B7.28c GEO profiles
PInt SPBP8B7.28c Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBP8B7.28c Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBP8B7.28c Fission yeast phenotypic data & analysis
Cyclebase SPBP8B7.28c.1 Cell Cycle Data
SPD / RIKEN07/07D12Orfeome Localization Data
UniProtKB/SwissProtO94276Meiotic chromosome segregation protein P8B7.28c
ModBaseO94276Database of comparative protein structure models
STRINGO94276Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596535LIM-like protein linking chromatin modification to RNAi, Stc1
RefSeq mRNANM_001022456972h- LIM-like protein linking chromatin modification to RNAi, Stc1 (stc1), mRNA
ePDB2LUYThe European PDB
PDB2LUYPDB
PDBsum2LUYPDBsum
European Nucleotide ArchiveCAA21813.1ENA Protein Mapping
UniParcUPI000006B57EUniProt Archive

Literature for stc1

Search: Europe PMC or PubMed

Release Version: PomBase:30_60 - 12 May 2016